gulnazzaidi/casper-r repository overview

⁠CaSpER CNV Analysis – R 3.6 Docker Image

This image provides a R 3.6.3 environment for running CaSpER (Copy number Analysis of Single-cell Expression in R) with all required CRAN and Bioconductor dependencies installed.

⁠Image Details

• Base R version: 3.6.3 (2020-02-29)
• Bioconductor version: 3.10
• Primary package: CaSpER
• Docker image:

⁠Installed R Packages

⁠CRAN Packages

• ggplot2
• reshape
• pheatmap
• RColorBrewer
• signal
• mclust
• scales
• gridExtra
• limma
• ggpubr
• igraph
• intergraph
• optparse
• getopt

⁠Bioconductor Packages

• IRanges
• GenomicRanges
• GO.db
• org.Hs.eg.db
• GOstats

⁠GitHub

• CaSpER (akdess/CaSpER)

⁠run the container interactively

docker run -it gulnazzaidi/casper-r:v3.6

⁠Run With Mounted Host Directory

docker run -it --rm
-v $(pwd):/work
gulnazzaidi/casper-r:v3.6

⁠Run an R Script

docker run --rm --entrypoint Rscript \
 -v $(pwd):/work \
gulnazzaidi/casper-r:v3.6 \
/work/your_script.R

version 3.9 has additional procps installed